


Nanite Entanglement

by lindaljc



Series: Nanite Entanglement [1]
Category: Stargate Atlantis
Genre: Action/Adventure, Angst, Atlantis AI, Bad words that everyone's heard if not said., Cut off from Earth, Drama, Elizabeth Weir: friend or foe, Gen, Graphic scene of death, Horror, Nanites not Replicators, Team, Unknown Characters Death, gen - Freeform
Language: English
Status: Completed
Published: 2019-03-11
Updated: 2019-03-11
Packaged: 2019-11-15 18:59:37
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 10,239
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/18079091
Author URL: https://archiveofourown.org/users/lindaljc/pseuds/lindaljc
Summary: They had no idea what effect this mission would have.





	Nanite Entanglement

**Author's Note:**

> The Sweet Spot of Characters plus some regulars and a special appearance: Sheppard, McKay, Emmagen, Dex, Weir, real Carson, Lorne, Radek, Chuck, Bates, also General O'Neill  
> Disclaimer: The characters and settings of Stargate SG-1 and Stargate: Atlantis belongs to Showtime/Viacom, MGM/UA, Double Secret Productions, and Gekko Film Corporation. All other publicly recognizable characters, settings, etc. are the property of their respective owners. The original characters and plot are the property of the author. The author is in no way associated with the owners, creators, or producers of Stargate: SG-1 and Stargate: Atlantis or any other media franchise. No copyright infringement is intended.  
> This story was written by linda.ljc with the love of the show in mind.

..........

The mission scheduled that day caused some worry for the team as they stepped through the Gate. It was always a bit of a crap shoot how good or how bad any contact through the Gate went. Because, really, there are all kinds of crazy that can happen, and AR-6 hadn't reported in on time, so it probably wasn't good. 

They didn't know it but this mission was a turning point for the Expedition. It could have broken hearts and souls, and perhaps it did. Things were never the same. It should have probably finished the Atlantis Expedition. But the truth was that the fate of a galaxy may have just turned on a dime. 

.........

Sheppard's team stepped through the Gate, which unfortunately left them face to face with the natives, and nothing ever went so wrong so fast. They didn't even get to say "hello" first. 

"Sheppard," hissed McKay as all their weapons came up to the ready position, even Rodney's.

"I know. Everyone, by the book. Safeties off." Sheppard looked like his well-known slouch was turned inside out, and he looked lethal as hell. 

The natives took notice but their "chief, headman, dictator" smirked. He knew he held the high ground here. The DHD, their ticket home, was between them and the team that had just arrived, and it would take precious seconds to dial and connect to wherever they needed to go. 

And there on the ground, laid out like animals, was AR-6. At least they were assuming it was AR-6 from some of the equipment and uniform pieces thrown in with the meat. 

Rodney McKay tried to keep his horror to himself. This wasn't a rescue mission now, they just needed to get home themselves and it wasn't looking good. He swallowed heavily and paid attention to Sheppard, waiting for a sign, some signal. 

Sheppard stared at the leader for a moment more, perhaps needing that moment to compose himself and his voice. "We came to see where our people were. We can see what you've done. What we want to know is why?" The tip of his weapon rose just a bit to emphasize his ready position, and reinforcing their "preparedness" to stand their ground even though their position was pretty much indefensible. There wasn't much else to do considering all the weapons aimed at him and his team, even though they were not projectile weapons. He hoped to encourage an answer to his question at least before the attack started. 

Headman jutted his chin higher. "You are not welcome here. You bring your weapons and your demands where they are not wanted."

Sheppard's fury was beginning to get the best of him. He snapped angrily, "They wouldn't use their weapons unless attacked. And we make no demands. We only ask for trade or alliance or both. Why did you do this..."

A faint whistling sound was the only warning as Sheppard collapsed silently into Rodney's arms. Ronon's gun tracked around the crowd as did Teyla's trying to find an obvious target.

The headman raised his arm and surprisingly his people lowered their weapons.

Rodney was frantically trying to lower Sheppard to the ground. "Sheppard! John! Speak to me! Oh, damn, oh damn. Ronon he's, he's not breathing..."

The headman spoke one sentence and all of the natives faded into the forest. "You may leave with this message: do not return."

It seemed that the tiny dart that had pierced Sheppard's chest was more than enough to kill a man. Rodney pulled it out as carefully as he could and threw it down. Ronon stood back as Teyla joined Rodney in trying to see the damage and take action, but there was little to see.

Rodney turned confused eyes to Ronon. "I, I think it's poison. I don't think I should have touched it." With that, he settled to the ground still holding Sheppard but weakly gasping for breath. 

Teyla looked down at her hand that had touched the wound. She looked up at Ronon in horror. "Open the Gate, Ronon. Get us out of here."

Ronon looked grim as he glared around the clearing, but the natives were still gone. He stepped to the DHD and entered the address for Atlantis then sent the IDC. He turned back to his team mates and yanked Teyla to her feet and then Rodney. He thrust McKay into Teyla's arms and told her to hang on to him. She managed a nod. He didn't know what was on the dart but he felt some of it's effects just by touching Teyla's and Rodney's hands.

He bent to scoop up Sheppard but glanced at the dart. Hopefully it would be of some use. He grabbed the blunt end of it as they all stumbled through the Gate. 

Ronon stood swaying on the other side. He lowered Sheppard to the floor, then he threw down the dart and dropped to his knees. Marines stationed around the Gate rushed forward. 

"Stop! Poison dart. Don't touch it or us without protection. Only Sheppard took a direct hit."

Everyone stopped, and it was a good thing because the lights went out. Even emergency lighting stayed off. Ronon finally collapsed into that darkness not knowing what followed until later. 

From everywhere in the Control room could be felt a faint vibration and the sound like many hundreds or thousands of scurrying metallic ants. Slowly the eyes of the people in the Control Room adjusted to the gloom and they could only gasp at the sight they saw. The floor undulated faintly as millions of tiny nanites converged on the team. They converged first on Sheppard until he couldn't be seen. Then other nanites chose their team member to engulf. 

Elizabeth stepped back, and back again. It was a horror worthy of the darkest nightmare, and she wasn't alone. Everyone moved as far as they could. The Marines on the Gate floor were ignored by the nanites, and when the guards could maneuver around them to get further away, they did. 

Chuck's eyes were wide and he ignored all the questions coming over the com. 

The nanite "mounds" ebbed and flowed, pulsating like a breathing being. 

Elizabeth trembled at the sight but finally regained her voice though it shook as well. "Chuck, get Dr. Zelenka up here and anyone else he wishes to bring. Call Major Lorne and explain the situation as best you can. Contact medical, I have no idea what they'll need to bring though. Get the Hazmat teams in place. Put out a general alarm and tell everyone to shelter in place. Go."

Chuck whispered a "yes, ma'am" and turned to his board. 

Being the Second in Science, and with McKay off planet, Radek Zelenka was quick to make an appearance but at this point he wasn't very helpful. He first had to observe, and contain his shock and revulsion at the scene on the Gate Room floor. "Oh můj Bože." As his understanding grew, he ventured onto the floor.

Elizabeth whispered, "Radek?"

"Is alright. I think. They are nanites. But what are they doing here?"

"Nanites," was followed by a shuddering sigh. "It's Sheppard's team under there. They came through, collapsed, and Ronon said they were poisoned."

"That was when we lost the lights, yes?"

"Yes. We didn't see where they came from, but we heard them. I wish we could see them. The team."

Radek rushed up the steps and Chuck moved well clear of the control panels the scientist would probably need to access.

With a barely there touch of a cable Radek started to connect his laptop but there was a slight spark. He stepped back in confusion, trying to understand this developement. Then a message appeared: 

overload imminent  
do not access.

Radek sighed. "Atlantis?"

radek wait

Elizabeth stared at the screen, not quite believing what she was seeing. "Atlantis, the AI, asked you to wait."

"Yes."

"Is it directing this, this, nanite infestation?"

"I believe so, Dr. Weir. I would hesitate to try to stop her." He shrugged his shoulders. "I don't know if I could, or should."

"But Sheppard's team..."

"Yes, Sheppard's team. But it looks like the nanites are working on all of them, yes? Should we stop them? Atlantis very much likes Colonel Sheppard and Dr. McKay especially."

"True. Stopping them might be impossible anyway."

"Jo... I must agree since Atlantis will not even accept connection."

It was a matter of waiting. The morning sunlight gave way to afternoon. With the growing shadows came an eerie glow from the floor of the Gate Room. Shift change for those on duty came and went, but everyone held their places with only short breaks taken when needed. 

Elizabeth didn't usually pace the Control Room, preferring to keep her worry out of public view, but she did that day, with a firmly held cup of tea in hand which had to be stone cold long before the situation changed significantly. She sighed as she stopped near Major Lorne and his team. "They went to rescue AR-6."

"Yes, ma'am." 

"Ronon wasn't able to give us any more information than I gave to you."

"Yes, ma'am. I don't hold out much hope for them."

Elizabeth sighed deeply, "Perhaps we should..."

"Ma'am, look."

The nanites in growing number flowed to the floor. About six feet away from the team they seemed to disappear into the floor without a ripple and only the sound of their passing. The last to leave took the poisoned dart with them.

"They're breathing." 

The team didn't move at first, then Ronon rolled over on his back with a groan. His confusion was clear to see as he looked up at the ceiling, and he made an abortive move to draw his blaster from it's holster, then made a clean move to sit up and twisted around to find his team. 

"Teyla, you awake?"

Teyla could be seen to take a deep cleansing breath and her eyes immediately sought Ronon's. She twisted upward and reached out to shake Rodney's arm.

Rodney bolted upright and started to hyperventilate. Teyla put a calming hand on his shoulder. Rodney looked around and saw that Sheppard wasn't upright. The rest of the team gathered around him, and they each looked to the others. Rodney took a deep breath and reached out. Before he could touch him though, Sheppard bolted up to stand ready to take on an attacker when none was now present. 

McKay grinned, "He's alive!"

"Of course I'm alive. Wait. Did that really happen?" Sheppard patted his chest. "Yeah, I'm good."

"We made it back."

Elizabeth broke in, "Yes. Do you know what happened?"

Sheppard turned grim in an instant. "AR-6. They butchered them."

"Oh, my God. Did they say why?"

"They didn't like our offer of trade or alliance. They felt we would steal from them or coerce them. I don't know." 

"I'm so sorry, but they will have to be dealt with, later."

Rodney glared. "We need to send them a nuke."

"Rodney..."

"No. You didn't see them, Elizabeth." 

And Elizabeth didn't respond. She could see the devastation on his face; on all their faces. 

Ronon gave Teyla a hand up off the floor. "What happened when we got back? All of us, we were dead or dying."

Sheppard looked surprised at that. "All of us?" 

Rodney nodded once at him and stated matter-of-factly, "You were already dead." 

Sheppard rubbed his chest again. "You were all shot, too?"

Teyla answered him this time. "No. But the poison from your wound transferred to Rodney and I when we touched you and the dart. Then I think, it was transfered to Ronon when he got us through the Gate."

"Then... what happened when we got back?" And everyone went silent.

"Come on. What happened?" Rodney glared at everyone. "Radek? Well?"

Radek sighed mightily. "Come look. All of you. Maybe you can tell us."

It was a confused team that headed up the stairs to the Control Room. The panel was still lit with the warning: 

overload imminent  
do not access  
radek wait

"What's this?" Rodney glared at Radek.

"I was not allowed to connect laptop to Atlantis controls."

"What do you mean allowed?"

Sigh. "Rodney... it said my name. Besides, you did not see what we saw." He approached the panel and Atlantis' message disappeared. He tentatively entered a command to replay security footage. 

Sheppard shuddered hard. Teyla wrapped her arms around herself like she was cold. Ronon leaned in to place his arm around her shoulders to share a little warmth and comfort with her, and Rodney sat abruptly in Chuck's vacated seat and wanted to put his head between his knees, but he watched till the end of the feed. 

..........

They spent a very long time in the infirmary and didn't complain. They'd seen the looks on everyone's faces. Even if they were cleared, how could they be sure? There could still be nanites running around in their system. Heck, nanites could be holding them together, making their hearts beat, making their brains... not their own? That was the fear, that they were not the same people. They could not be trusted... ever... again.

Complaining would have been a waste of time. They had a lot to think about. What were they going to say to the SGC? How could they prove the unprovable? How do you prove that you're innocent when the "contaminant" can change your actions, your very thoughts?

..........

Elizabeth looked dumbfounded. "They've been there for hours and they didn't complain? Not once?" She sighed worriedly. "They always complain."

Radek was with her and Lorne in the conference room. "Do not take that as a bad thing. Remember, they have much to think about. And they do not want to interfere with or even delay their release."

"How do I explain this to the SGC? What will they decide when given this information?"

Radek sighed as he leaned back in his chair. "They will be afraid. They will be very afraid. Atlantis chose this course. They will be afraid of the city and what it might choose to do in the future."

..........

Sheppard, McKay, Emmagan, and Dex sat quietly while tests were run, and run again, and tweaked, and run again. When the doctors and nurses were doing their "thing" the team mates didn't even glance back and forth. 

Their minds were going a mile a minute, as the saying goes, not just thinking about their new situation, but also about their connection to each other. They were different and it scared them silent. Atlantis was so far, a silent, fifth "connection" whose interference had now allowed a certain amount of mental connection between the team mates. Because of the nanites. Because there were some still there. They all expected the doctors to acknowledge it in some manner but nothing was said about them. And that was bad, because that meant they couldn't be detected, and therefore they all were suspect, were compromised. And that meant untrustworthy.

They learned from one of the doctors after the first tests that they all had the ATA gene, all of them, a better gene. But mental connection between carriers was not a trait known to any of the Ancient's descendents from Earth until now. That wasn't good either. Oh, it could be useful, very useful, but suspect.

When Atlantis opened a dialogue with them she made them see the possibilities. She told them her side, that she had been aware of them since the Expedition arrived. She hated withholding the nanites because she could have used them to help, but she knew how the Ancients had felt and was aware of the Tau'ri prejudice against their use in biological organisms. But she might have saved lives and that made her especially protective of these four. There had really been no choice. She had to save Sheppard, even though she knew others of the Expedition had a form of the ATA gene. 

Teyla's and Ronon's thoughts were wild and fearful at first. John and Rodney had at least a fleeting experience of the gene. Atlantis spent some time trying to calm those fears although they were not unfounded. They all, to some degree, felt trapped in their new situation. 

Finding that the team was now ATA capable was incredibly concerning to the medical personnel. With the interference of the nanites they were no longer human, or Pegasus human, even without evidence of the nanites themselves. 

Everyone's greatest fear was that they could be controlled by Atlantis, and not even know it. But all the while, Atlantis denied it, explaining that that very fear was why she had waited to initiate contact with the nanites. But John Sheppard was the AI's best hope to make war on the Wraith. The descendents had come back and Atlantis wasn't going to let go easily.

They finally were as fully cleared as the doctors could come. There was an oddly silent trip to the conference room to debrief. They entered and sat in their usual places.

Those already there glanced uncomfortably to each other until Dr. Weir awkwardly cleared her throat. "Well... you've been cleared by Medical..."

Sheppard nodded gravely. "You know we're still us, Elizabeth."

She started to nod but stopped and clutched at her laptop. "No. I'm not sure. And I don't know how to ever be sure again. Your medical reports say you all now have the ATA gene, and it seems to be a better version. So we know you've been changed. Altered."

"Without our permission."

She nodded slowly in agreement. "What else could be done without your permission?"

Rodney looked horrified. "But... we're us! Look at us. Talk to us. Test us all you want. I'm me. I'll always be me. If you don't believe us then how will the SGC?"

Dr. Weir nodded. "Yes, how will they? If Radek can come up with some immutable test..."

Radek just shook his head and wouldn't meet anyone's eyes. "Not possible. Perhaps Rodney could..."

Dr. Weir interrupted, "Not Rodney. He can't... be trusted."

Rodney's dismay was pure grief. He knew better than anyone just how her statement would be taken. Because of the AI's interference they could be lost to Atlantis, or Atlantis lost to them.

Sheppard clasped his hands and began telling Atlantis' side. "It was to save our lives. She wouldn't have interfered if we weren't dead or dying. She made changes in us, but she explained to us how it could be beneficial to us, to the Expedition. She could give all of you the ATA gene. That alone would advance our efforts a hundred fold."

Elizabeth slowly shook her head. "Is she listening to us even now? Are the rest of us going to have a choice of accepting the changes or is it her will that will prevail? There are so many questions, and no matter what you believe is true, is there any way for you to know for sure that it's your true understanding... or is it Atlantis'?"

There was silence as the four team mates began to understand just how futile their situation was.

Elizabeth ventured an important question that needed an answer, whether they could trust it or not. "Do you still carry the nanites within you? There was no medical evidence they could find."

McKay dropped his eyes. He knew they could give away everything and still not be believed. He let Sheppard answer.

"Yes, Elizabeth. It allows a closer connection to Atlantis. It's not as vague a connection as before. It's not telepathy by any means, but information can be passed more easily."

"I see."

Ronon leaned forward. His intensity was honest. "Will you make us leave?"

Beside him, Teyla, was pale. "Or will you send us to Earth? I do not think we will be safe there. John?"

"We won't be going back to Earth, Elizabeth. She's right. They could take us apart piece by piece to see how we work."

"I'd never allow that, John."

"You might not be here to make that decision, you know. You, too, can be replaced. You know it even if you don't want to think about it."

Radek cleared his throat softly. "I do not think we need to worry that the SGC will try to steal you away. They do not like encounters with nanites and their big brothers the Replicators. I do not know what they will wish to do. They have many more paranoid minds there, than here."

"We can't make a final decision without contacting the SGC. We'll see what they have to say after they see the report." Elizabeth clasped her hands on the laptop in front of her. "I want to say that I believe you aren't a threat, but I'm only human. You may not be anymore. Still, I have trusted you this long and it's hard to let that go, because I don't want to lose any of you. I want you to remain on Atlantis, but it may not be my decision, as you say, John. But we'll continue as we have for the moment, but don't think you won't be watched. But you're our leaders, our friends. We have depended on you for our lives, and I don't think that will change. After our reports are sent to the SGC we'll see what options are available to us."

Lorne cleared his throat, "Perhaps we could discuss AR-6 for a moment? What happened out there? Who poisoned you?"

Sheppard leaned forward. "We have the video from when we went through the Gate, but we know the one most responsible."

Rodney muttered, "You can see what they left of them on the video." He looked to Weir. "I know we've discussed this before but we can't let them get away with four murders. If we can imprison the worst of them somewhere then maybe the remainder of the population would be a little less bloodthirsty."

Ronon grunted. "What's the chance?"

But, it was better than a nuke, which wasn't a real possibility anyway. There were innocents in their village and no one really wanted to enact that level of revenge. It would make them the monsters.

..........

The Gate to Earth was opened that day, after the reports and messages were readied. It was late in the day but they didn't want to delay, late though it was on Atlantis and it was even later on Earth. But they didn't have long to wait for an answer as they were woken before their dawn. Unfortunately their assessment of the SGC's and the IOA's response was much too understated. Radek had been closest in his assessment. 

The timing worried everyone, and Dr. Weir tried to compose herself as best she could in her robe and pjs, before she spoke. "General O'Neill. We weren't expecting a reply so soon. Considering the news we reported we expected the IOA to remain in conference for a while. Is there more information we ca..."

O'Neill's military bearing was making Sheppard nervous. The man was known to slouch on occassion and there were no "pie" jokes. The man had "tells" and they were all deeply controlled. So, this was going to be bad.

The General interrupted Elizabeth. That also was unusual. He was often gruff but generally chivalrous. "The IOA went into emergency session immediately after your reports were scanned. I'm sorry to say that... " O'Neill shook his head sadly and let himself unbend a little. "Look. I'm more sorry than I can say, but their decision is final. Four of your party have been compromised with nanites. There's no going back from that. It's a fact, and there's no way they'll accept further contact from Atlantis. You are all suspect, not just the four knowns. 

"I'm sorry, but you're quarantined. You'll be locked out of the Gate in the Milky Way, and if you ever find a way to return to Earth, you will be considered... invaders; enemies on par with the Replicators. They won't even allow messages to be sent in case you try to, I don't know, give us a virus, take over the Gate, or the world. Who knows what their minds have come up with? 

"Just know that we're sorry as hell this happened. We always meant to stay in contact, but you're on your own, Atlantis.

"We'll increase our watch for the Wraith. We know they're still hunting for Earth, and I've recommended precautions to protect Earth, or at least warn us if they get too close. Or if you get too close. That's the best we can do for now. 

"And I, and everyone here at the SGC, wishes you the best."

O'Neill turned away. "Walter, close it down. Lock it out."

O'Neill turned back at the last moment and snapped a salute before darkness filled the Gate with finality.

Elizabeth could barely speak at first, such was her shock at this development. "No. But..." She turned to the others on the Control Deck. "John? Rodney? How can they do that? We, we're not infected with nanites. How can they do this?"

"Elizabeth..." Sheppard was cut off by her shocked reaction.

"NO. Chuck get them back. Open the Gate for another message. We... They have to know they made a mistake! We have to tell them; convince them."

The Gate lit, dialed, and died. 

Elizabeth was furious. She slapped her hands down on the railing. Then she turned on John, who was closest. She slapped him. She would have done it again but Rodney caught her arm. 

Rodney stood there clasping her arm but he turned to Sheppard, "John, you can't let her do this. It's not right. You don't deserve this." He turned to Elizabeth and shook her arm once, twice. "You didn't think this through. They have no way of knowing how many are truly compromised. I know it's not your fault. It's not his fault. But this is what we have." He slowly lowered her arm and let go.

Elizabeth wrapped her arms tightly around her torso. Her eyes closed and she shuddered. When she looked up her hand went to her mouth and she whispered, "Oh, John. I didn't mean it. I'm so sorry."

Sheppard managed a nod before walking away.

..........

"Of all of the worst case scenarios, I never, really, seriously, thought we'd be under quarantine from Earth," Lorne murmured to the group at large. The conference room was crowded. Everyone wanted to know the plan for the future. Could there be a future without resupply from Earth? The last resupply they'd received from the Deadalus would keep them from having to scavenge for a while, but they had been pretty low before that.

The doors swished open and the Sheppard Team arrived together. They seemed to do everything together. It kind of creeped people out. It made them doubt them, and what was needed was trust.

The team found seats around the table and though it was crowded, the seats near them emptied. Sheppard could be seen to sigh before looking to Dr. Weir and Major Lorne. "May I speak?"

Weir looked embarrassed. "I really didn't mean my outburst earlier, John. I want to apologize formally, here and now. You didn't ask for what happened to you or your team. You were doing your duty and you would have died without Atlantis' intervention. And you certainly didn't ask for the decision they made on earth.

"Maybe we should have tried to keep this secret, but there were just too many witnesses. Maybe a delay would have given us more time to plan, but they would have been suspicious of that, too. I certainly never expected the IOA's reaction... and maybe I should have. 

"I just couldn't believe that they would turn on all of us, the whole Expedition. I can't believe I didn't even see the possibility. I'm the so-called diplomat, and I should have known that their fear, their paranoia, would seriously affect their decision-making. I hope you can forgive me, because they did to us what we did to you."

"I... We do understand. We thought... we hoped, we could function as usual, and that was a stupid assumption. Like you said, fear and paranoia deeply affect our decisions. I can't say that we don't feel it, too. Looking around at all of you and knowing you don't trust us, well, it's hard to adjust to. And as many times as I say we're the same, we all know we're not." There was a murmur of voices that interrupted for a moment. "Look, the nanites changed us in a few ways and most of it was to save our lives. If you'd like us to explain further then maybe it can help us move forward."

Carson leaned forward slightly to add a comment. "Colonel, I know I need to understand the particulars and I'm sure everyone here would like more information. If ye'd share with us, it could help."

Elizabeth was oddly silent for a moment and looked distracted. Then she seemed to settle and she unclasped her hands. "Yes. That would be good. I think this is a need-to-know kind of situation."

Sheppard glanced to the side to his team. "We're all happy to discuss this Elizabeth. We can seriously plan for the colony that was always in the back of your mind. There are still the Wraith, but that's a problem perhaps of generations. Atlantis thinks if we allow the integration of necessary nanite repairs, we would have an advantage over the Wraith. Atlantis was very excited about the Spot-Shield* that McKay and Radek are working on, and, well, Atlantis has come up with a nanite version if we volunteer to accept it. It would prevent a hand-feeding by a Wraith like the little shield. We knew when we came here that we might be on our own from the beginning... and now we know. At least now, Atlantis would be free to offer her help."

Elizabeth again looked distant as she thought. Then she nodded vaguely. "Perhaps this situation is too new. We need to adjust and think about the possibilities for a while. I'm all for waiting till we've digested this. Perhaps your team could stay and give Carson the information he feels he needs. We can meet tomorrow to discuss this in depth." Elizabeth then rose abruptly and departed with her laptop.

Sheppard's team weren't the only ones surprised. Everyone had come hoping for a discussion that would be fruitful and address their most important concerns. John looked down at his own laptop. "Well, folks, it seems this meeting is over. Perhaps we can make some decisions tomorrow. Think over what your major concerns are and send an email to... Lorne. That okay with you Major?"

Lorne was jolted out of his stare after Elizabeth and whatever deep thoughts worried him. "Yes. Of course. I'll, ah, write up an agenda for the meeting; make sure we try to answer all the major questions. I'll see everyone tomorrow." And Lorne left, too, followed by all the others.

"Well, Carson. I hope you don't mind being stuck with the four of us."

"Not at all. Did Dr. Weir seem a bit... off."

"Well, she's got a lot on her mind."

"Aye, well let's get down to it then..."

..........

Elizabeth watched as the others filed out of the conference room. Good. She had questions to ask of people that might be able to give her straight answers. Unbiased answers. Uncompromised answers. When she saw Lorne exit she nodded to him and gestured for her office. Lorne headed that way, but Elizabeth waited until she saw Radek. These two could hopefully supply the information she needed. 

"Gentlemen, please sit. As you might have guessed I have some questions I need answered." Both men looked serious as they glanced to the other. 

Radek said, "Dr. Weir, I wish to advise you that even we," and he glanced again at the Major and back to Elizabeth meaning her included, "are suspect. Any of us could have been compromised by Atlantis' nanites. I happen to agree, in part, with the IOA's and SGC's decision of quarantine. It is drastic and affects us dearly but they have had incursions and have fought for the Asgard as well against Replicators. We don't know where Atlantis would draw the line."

Elizabeth was clearly taken aback. "I think I'm far behind on understanding many of the ramifications of Atlantis' actions. I think I hoped we would at least know if we were compromised. You're saying we might not even know."

"Yes. Even if we know, we might not be able to communicate it. I hesitate to suggest that Major Lorne contact Atlantis in the Control Chair. I just don't know how safe that would be. Or if it is as safe as anywhere on Atlantis. It all could be inevitable, and unstoppable, but the Chair might give us information... if we can still trust the Major after. And trust, now, is a very slippery thing."

Lorne obviously considered the option. "I would of course do this if you wish. I can't guarantee anything but it might tell us some information. Maybe I can impress on Atlantis that this is not something we approve, and that it must stop."

"Radek, Atlantis must be able to hear us anywhere, not just in the Chair. Is that true?"

"Yes. If she wishes, and the connections are not jammed."

"Can you jam them, here in my office?"

"I'm not sure how secure it would be. Even with jamming, there are vibrations and reflections that she can probably interpret. Even on Earth they were getting more adept at that. Tecnology and spying have become strange but accomplished bedfellows."

"Then perhaps we can get her permission for what I have in mind." Elizabeth considered it for a moment more, then turned her gaze back to Radek. "Dr. Zelenka, I was wondering if we can... entrap the team in a containment field." Lorne looked alarmed and Radek looked thoughtful. "I don't want to hurt them. That is not my intent. I don't want to imprison them for any length of time. I just want to see if we can force Atlantis, or Sheppard and his team, to make the nanites leave their bodies. Radek, is that even a possiblity?"

"Well, with Atlantis listening, she could decide to interfere, or warn them."

"Yes. I can't change that, obviously. I want to trust Atlantis as well as Sheppard, McKay, Teyla, and Ronon. This isn't exactly a test for Atlantis, but maybe she could let us do this to give the team a chance to evict those nanites within them. To let them have a personal choice."

"It could be attempted, especially since you state you wish no harm to them. Maybe Atlantis would see our sincerity in banishing the nanites. Maybe it can take them back." Radek gazed around at the various walls. "Do you understand, Atlantis, that we mean them no harm?"

The lights blinked. 

Elizabeth nodded. "Thank you, Atlantis. Radek, I think you have some work to do. Major could you help him with this, if necessary?"

"Of course."

"Let us go, Major. I can be ready by morning, I think... a containment field that will let the nanites through the field..."

..........

It was a late night for Elizabeth Weir. Her thoughts were unstoppable, and each led down a dark trail of skittering metallic constructs. When she had woken for the fifth time to what she would swear was the scurry of ants – no, not as innocuous as earthly pests, but nanites. 

She finally gave up. She dressed and wandered her room, pacing what was left of the night away. She was so tired. And whatever Radek came up with, that was it. They hadn't thought of any other options but to let the Major sit in the Control Chair. She didn't want to allow it. As far as she knew, Lorne was uncompromised and she wanted to keep it that way. It was a risk for Major Lorne, and she didn't want to risk another of the Command Staff. 

Dawn was peeking through her curtains when she received the call that it was ready. "I'll be right there."

.........

"We are ready, Elizabeth."

"What is the target area? Where must they be to be enclosed in it?"

Lorne gestured to the base of the stairs leading to the Control Deck. "We'll need to get them all there at once."

Radek rubbed his tired eyes. "Hopefully, they are still staying in close proximity. Do they think we will attack them? Well, yes, that is exactly what we plan to do. And Rodney will never let me live this down."

Lorne directed Elizabeth to climb to the Command Deck. She would ask for their presence, and then Lorne's. He would hang back to allow the team to go first after Dr. Weir's request. Hopefully this wouldn't raise their suspicions or make them feel herded against their will.

Radek muttered worriedly. "I truly do not like this, but we have not many choices, I know."

Elizabeth looked worn, like she'd not slept any more than Radek or Lorne. "I'm sorry, Radek. They're our friends and this is a horrible trick to play... but this is it. We will know today."

Sheppard's team entered the Gate Room soon after. They spoke softly and didn't seem suspicious of any activity there. 

Elizabeth leaned on the railing above the Gate and asked, "Colonel Sheppard, could you and your team come to the conference room. I'd like to go over what you discussed with Carson yesterday."

"Oh course." They headed for the stairs.

"Major Lorne, perhaps you could come, too."

"Yes, ma'am."

It was just a few steps before the containment field lit with it's garish glow.

"Elizabeth?" Sheppard and the others on his team looked around in confusion. It didn't take long for the answer to occur to them. "A containment field." He was obviously furious, but he waved his team to stand down. "Why? What do you hope to prove? What do you hope to gain? Do you want to make us enemies? We have no where to go but here, in Pegasus."

"There are things we need to know, John. I'm sorry." She spoke firmly. "John, if possible tell the nanites to leave your body. If you can't or won't, I'm directing Atlantis to remove the nanites."

John was shocked, "But... no. Atlantis, you can't!"

Elizabeth wrapped her arms tight around herself. "Atlantis, tell the nanites to leave, please."

"Elizabeth, no!" squeaked McKay. "Radek, it's the wrong order! Make her stop it."

The lights dimmed and the team collapsed as the few nanites still in their systems were recalled. 

The team laid still as death. Not a breath could be seen or heard. 

"Radek? What's wrong? What's happening?"

"I do not know. I need to check the readings from Atlantis."

do not connect  
overload imminent  
radek wait

"Ah, the same as before." He glanced at his friend McKay and the rest of the team in despair. 30 seconds. 1 minute. There was no time to wait.

He forced a manual connection with a resultant cascade of sparks and violent sounding alarms. The shock knocked him off his feet for him to land near the stairs. The containment field flowed gently to include him, and the metallic clicking and skittering sounds filled the area around the field. They rose from the floor and through the field as if it didn't even exist, which was exactly how it was designed by Radek. It now engulfed the team and Radek, too.

Dr. Weir spoke softly, and only the Major heard, "Oh, what have I done?"

The same process of repair seemed to occur but not much could be seen. When the nanites left... the five members in the containment field slowly came back to life as the field faded away. 

Dr. Weir stood in the Control Room and spoke to Radek and those affected on the Gate Room floor. "Could we all gather in the conference room. Some discussion is required, I believe."

Sheppard spoke harshly, "Ya' think? How about a little discussion before you attempt something that could kill us?"

"Please. The conference room."

Sheppard snapped bitterly, "Of course, Dr. Weir. Of course."

They settled in their familiar seats, and the silence was unsettling.

Elizabeth cleared her throat. "I don't know if this is a stupid question or not after this morning, but, there are still some nanites in you, right? Can you... have you... asked the nanites to leave? Or will Atlantis not allow it?"

Sheppard sighed tiredly. "It would have been nice to be asked before this... attack this morning, but the answer for me is... no, I haven't asked them to leave. As I think you proved a few minutes ago, I wouldn't survive. Ronon and Teyla got the lightest dose of poison, so maybe they can live without the nanite support. I know I can't."

Rodney shrugged a shoulder and added his own answer, "I can't either." Succinct for him, indeed. 

Ronon leaned forward to add, "I don't know about Teyla, but the damage done to my body would make me an invalid."

Teyla looked wistful as she added, "I could probably never have a child, and my life would be shortened and filled with pain."

Elizabeth leaned back. She looked defeated; worse than defeated. They were her friends, and what she had done was a dark betrayal.

Teyla stood. "Dr. Weir, we have never been your enemies, yet you gave us no chance to prove ourselves. Now I find I need time and space to gather my thoughts and emotions. To make as much peace as I can with what has happened. I am requesting a visit to the mainland if it is allowed."

Dr. Weir started to shake her head, her denial on the tip of her tongue. 

Sheppard stood beside Teyla and so did McKay and Ronon. "We are going to the mainland. We need a break. So do you. Decide what you have to decide... and get back to us." He turned to Radek, "Doctor, you're welcome to join us."

Radek took a long look at Dr. Weir before deciding. "I might be of more use here. I can answer questions if need be."

"All right. Call if it gets too bad, okay. I'll come get you." Then the team left. 

Elizabeth's thoughts were focused far away and she belatedly nodded her approval, but they weren't there anymore. She soon heard a flight request to the Control Room, and the team was on their way.

..........

Elizabeth sat in her office the next day. Her tea was getting cold and she was slowly pulling her muffin apart as she pondered many things. Certain of Sheppard's words kept going around in her head and she hoped they were true. They could make a life here, a colony like she had in her most starry-eyed plans. Their permanent home was here in Pegasus now, so things were going to change. There was no choice. No going back. So she'd better get her head in a better place. She hoped she was up for the challenge, but she also knew that there were people she could lean on. She just needed to apologize to them. Again. Making amends was going to take a while.

When she finally stirred she contacted the mess hall. "Can you have coffee and snacks ready in about an hour and a half? I'll be calling for an informal meeting in the mess hall of everyone that can get away from station." With that set in motion she requested everyone's presence for the meeting. Then she called the mess hall back to request hot and cold foods and beverages to be ready after the meeting for a trip to the mainland. Making amends would necessarily start out small, but good food never hurt. And coffee, of course.

Elizabeth left her office to put on traveling clothes and sensible mainland type boots. Then she called Radek, hoping he would join her after the meeting to visit their missing team. 

She reached up to touch her mic. "Major Lorne, there will be two to travel to the mainland after the meeting. Can you provide a pilot?"

"Of course." Lorne suspected who the passengers would be so he chose to do the ferrying himself. 

.....

Elizabeth found it hard to keep away from the mess hall until the specified time, but she knew people would arrive in small groups and eventually get settled.

When she walked in she headed to the hot drinks and made herself a hot tea, and added sugar. She might need the energy since most of the muffin from earlier hadn't been fit to eat. While she stirred her tea she listened and watched. Everyone seemed calm which was good. 

She finally headed toward a table near the back where she often sat, but today she perched on the table and rested her feet in a chair. It was a very casual pose, and calculated to be so, because this was an informal meeting. She needed honest responses, and people needed to feel free to make them.

"Good morning, everyone." There were lots of murmurs and nods and she nodded back. "I guess it's about time to have a general meeting. We all know the IOA's and SGC's decision. And we know there's no going back."

That was met with some bleak looks and Elizabeth tried to meet as many of their eyes as she could. "I know my own reaction was an overreaction. I regret it, especially since I should have seen the possibility, but I can't change it. It's simply how my own shock and surprise manifested itself. I'm not very proud of it, but I have to live with it and make amends as best I can."

Sergeant Bates raised his hand and Elizabeth nodded for him to speak. "Dr. Weir, we've all talked. We've asked the scientists to explain. Do we have it right that Atlantis did this? Gave us the nanites against our will?"

"Yes. That's my understanding."

"Then why is Sheppard's team on the mainland? They didn't do anything wrong."

"Again, you're right, Sergeant. I'm heading to the mainland after the meeting to talk to them. I'm hoping they're ready to come... home."

Elizabeth was pleased at the response. Marines and scientists alike were voicing their approval. It seemed there was no doubt on most people's part that the team was wanted and trusted no matter the nanites they harbored. "I really need an honest answer to an important question. Do you fear the nanites, or Atlantis?"

There were a lot of glances around and a little discussion but she waited for answers to be voiced. 

Chuck looked around and finally stood. He felt a little self-conscious. "I was there that day. In the Control Room. Sheppard's team was so still. I was so afraid we'd lost all of them. The nanites were frightening, but mainly because of the SGC having to fight the Replicators. These... constructs... are from Atlantis. They're not the Pegasus Replicators that the Ancients created. If they're controlled by Atlantis, then maybe they're not the nightmare we've come to expect. I'm not afraid of Atlantis. I don't have the ATA gene, but me, and a lot of others would take the chance. It would be extremely helpful. I'm not saying everyone should get it, and certainly not if they're against it. But maybe a trial by a few. I know Radek got it, and don't deny it Doc, but I seem to remember a little "happy dance" the first time you connected with Atlantis."

There was a growing surge of laughter at this, and Radek, who had taken a seat in an out of way spot, flushed with embarrassment. Elizabeth managed not to laugh outright in relief. 

"I'm glad to hear you're not afraid of Atlantis. We did give her a chance to interfere in the use of the containment field, but she let us have our trial without warning the team. She was working with us. And yet, as hard as this is to say, this could still all be directed by her. But we either stay, or evacuate; we either believe she wants us to choose what's best or she'll direct our future as she sees fit. I... want to believe. I... want to trust. If you can't, I do understand. We can make arrangements somewhere, perhaps with an ally, or on a totally new planet. But Atlantis wants us, and I choose to stay. Think about it, and let one of your supervisors know if you opt out. That is your choice.

"Well, I have another meeting to get to. Hopefully our missing team will be back soon."

.....

The flight was uneventful and Lorne set them down within sight of the Athosian village. Sheppard and his team mates met them, which was good because there was a lot of food and beverages in several large crates. 

There was a secluded area that Teyla directed them to. She wondered, as did the others, what the discussion would reveal. It was obvious to them that this was a little bit of a peace offering by Elizabeth.

There were some unusual things in the crates like blankets, even pillows, along with the utensils and fresh foods, bread still hot, and beverages from the mess hall. 

Sheppard joked, "You know this means I'm putting you in charge of supplying missions. This is much better than we usually get."

Radek grinned as he added, "Yes, if I could expect this I might fight Rodney for off world missions."

McKay glared at him, "Watch what you wish for."

Ronon and Teyla just watched the byplay without adding to it, waiting for the serious business to begin. 

Sheppard's smile fell away and everyone just waited until he looked up. "Hmm, I'm hoping this isn't a nice way to say we can't come back to Atlantis."

Elizabeth looked a little surprised. "That... no, that's not what this is. I thought we could sit and talk without so much pressure. We really need some long term plans and out here, away from the city and it's influence it might be..."

Teyla looked angry and interrupted. "Dr. Weir, we carry the city with us. There is no way she will not hear as long as we are on this planet. And if we are not to be trusted then how can you trust that Atlantis will not influence our discussion?"

"Oh." She shrugged as she admitted, "I really did think that was likely from what Radek and I have discussed. I was thinking more about the pressure of the people. But we had a meeting this morning. It was a good meeting. Most are quite accepting of Atlantis' actions, and wonder when our missing team can come home." She looked from Radek around the circle of very serious faces. "I was wondering, did you know that Atlantis was aware of the containment field experiment?"

McKay glared again at Radek. "Yes, after the fact, and there being a traitor I could name right here eating our food. Although, to be honest, she didn't warn us and she could have."

Sheppard added, "Maybe she wanted you to know there wasn't going to be a Hail Mary for this situation. There wasn't a way out of this even if you let us die. That there's no going back even then. Earth will never open a door for us again."

"Well, I've all been thinking a lot since you left. You were right in that, Teyla. We all needed some distance to hear our own thoughts on the situation and what it will mean in the future. I'm sure I don't understand all the ramifications of these changes, in you, and in Atlantis. But I want to. We are in this together, no matter the changes. If more are to come, and I'm sure there are, then we'll all have to cope as best we can. As I learn more, understand more, then maybe I can be more help than hindrance. You're not just colleagues, I hope we are still friends. I do hope that you know you can confide in me. I hope you can trust that I'll try not to make a snap judgement. I've learned a little more about our situation, but if there's something more I or anyone on Atlantis needs to know I hope you will pass it on to us. If Atlantis is to be a colony... we need a free flow of information."

The team looked a little guilty.

"There is something. Right? I meant what I said. Whatever you say will not be judged... and remember, we never have to make another report to the SGC or the IOA. They threw us all away. That's their decision, but ours is to deal with it. Together."

"McKay."

"Why me? Okay, okay. See, we're not really the first to be repaired by nanites. We were just the obvious ones."

Elizabeth's eyes rounded in surprise. "There are others with the nanites in them?"

"No. Not now. You see, if someone was alone and was injured it was easy for Atlantis to "fix" them. Sometimes when someone had a really bad injury and they healed much better than Carson expected, well, they probably had a little nighttime help, and then the nanites were recalled. Atlantis can, and has recalled nanites after their function was fulfilled. And no one was permanently altered... you know, given the ATA gene, because that would have been a dead giveaway that something had happened out of the ordinary. You don't have to worry, we're the only... compromised people on the city. And actually, Radek doesn't have any in him now."

Radek looked grateful, "Yes. I know that."

Elizabeth looked more surprised. "Why didn't you say so?"

Radek looked grave as he responded, "I am now ATA positive so there was no way I could prove it. My word would not have been trusted."

"Oh." Elizabeth sat for a moment with her eyes downcast. "I'm so sorry. I was just so focused on the idea that Atlantis would try to control you, and all of us, that any autonomy we had would be a sham. We would be worse than the Goa'uld, and more, we wouldn't even know it."

Ronon nodded. "Teyla and I were told a lot about them. Seen videos and stuff when we were on Earth. Maybe I begin to understand why you acted the way you did. I wouldn't want to live like that, a prisoner in my own body, forced to observe the evil that was done in my name. If I was forced to do evil when I thought it was not..." He hung his head as the thoughts were overwhelming.

Elizabeth whispered gently. "Thank you for that, Ronon." She glanced around the circle, trying to gauge their reactions. "I would like you all to return to Atlantis, when you're ready. Bates wasn't alone in wondering why you were out here when it was Atlantis and not you that did this. I think all of us on the city still have a lot to discuss, and decisions to make. Atlantis has made offers that some already wish to accept. And if there are some who wish to leave, I've offered to arrange a place with allies or elsewhere. We need you to come home."

Sheppard's features hardened. "One of the first things we need to take care of is AR-6."

Ronon added glumly, "I doubt there's anything left. It's been several days."

Elizabeth added firmly, "Then we exact justice. If this is to be our home, then we can't be seen as weak." 

She called Lorne for a return flight, and then they each stood to gather the crated items to be ready for transport. 

..........

The next day the team came to the Gate Room ready to depart. Sheppard looked at Elizabeth and asked, "Are you sure?"

She simply nodded assent. 

They were going to face the Headman on his own turf and they might need a little extra something. Atlantis dimmed her lighting slightly as scores of nanites moved to the team and were absorbed without a ripple. 

There were a few little gasps, as there were probably people present that hadn't seen the original scene although most people had watched the security feed. It was the most viewed piece of security video they had and the cause of many screaming nightmares. Beckett finally declared it off limits for the time being.

A cloaked jumper with Lorne and a team of Marines would accompany them. Hopefully they'd scare the crap out of the natives one way or the other. And then they'd snatch the top four, and perhaps one other if they could identify him, and take them into custody. 

The trip through the Gate wasn't met by the Headman's gang so they headed quickly inland.

When they walked into the village the natives encircled them shouting and jeering, and waving their primitive weapons until the Headman showed himself. He was furious as the team expected. But when he got a good look at them he looked more frightened than anything. It could be upsetting to see ghosts.

When he found his voice he called out, "You were told to stay away from here."

"Yeah, well, we got your message, but we thought we'd come back and propose a deal."

"Deal. You just want to steal from us."

"Nope. You see, that poison is pretty potent. It didn't kill us, as you can see, so maybe it would be a good trade item. We'd like to persuade you to share the details."

"The poison is our secret. Not for outlanders. You'll not get what you want from us."

Sheppard looked aside at Rodney, and McKay glanced pointedly toward the back of the crowd. He muttered softly, "The short one in the back, with the garish sash. There are minute traces of some of the compounds Carson told me to look for on his clothing. Everyone else reads clear."

The Headman was impatient with their chatter. He gave a signal and an attack was attempted with their darts once again. He began to grin as each of the team was hit with a small dart. The grin faded when Sheppard grinned back. 

They all plucked them out and dropped them into a bag they sealed. "It didn't work, did it? Your secret weapon doesn't work any more. Thanks for the samples though." He reached for his mic, "Lorne can you shoot the chosen ones, plus the chemist that mixes that vile stuff."

"Be glad to, Colonel." To the natives the flashes came out of nowhere since the jumper was cloaked, and the five men collapsed to the ground, stunned. The surprised and fearful villagers hung far back when the jumper uncloaked and landed, so when the men woke they'd been tied together, from one hand to the hand of the next, with zip ties. Those could be removed easily enough when they reached their new life.

Sheppard snapped to the Headman, "Say goodbye to your people. You won't be back."

The men really looked scared now but none on the Atlantis teams worried that they'd exceeded their reach here. Four good men were dead, and who knew how many others had succumbed to the poison over the years. These five would still have a life, as long as they worked hard. 

"Don't worry. We're not going to kill you. But imprisoning you for the rest of your life will have to serve as justice for the men you killed. We're willing to take two observers from the village. You won't know exactly where we leave your people but you'll see that they'll be left alive and unharmed."

Marines had come to prod the men into the back of the jumper, and two "volunteers" were wrangled to observe from the front of the jumper. The prisoners were soon deposited on a very isolated large island with a temperate forest on the other side of the world. It was easily a thousand miles from any other major land mass. Supplies and tools were left for them. And then they were left alone, and the volunteers were returned to attest to their disposition. 

While Lorne's team was busy, Sheppard's team had returned to the Gate and waited for their return.

..........

The jumper went back to Atlantis but returned soon with many mourners. The jumper lowered a huge round memorial stone where AR-6's remains had lain. Ronon had been right, there wasn't much left but a few scattered bones, but these people of the village would have to pass this two ton stone near the Gate every time it was used. It was made out of Gate material so it wasn't going anywhere without an awful lot of effort. 

It was embossed with the images of four men and the hieroglyph for the point of origin, Earth. It was a symbol unseen in Pegasus except on Atlantis' Gate. No one that saw it, or anyone they asked, knew what it was. But everyone remembered it, and the people that claimed it as theirs.

End

**Author's Note:**

> Point of Origin symbol from:  
> https://stargate.fandom.com/wiki/Point_of_origin
> 
> Oh můj Bože: oh my God  
> Jo: yes, yeah
> 
> Spot-Shield*: Mentioned in my story For Want of a GDO.


End file.
